噬菌体Z基因组生物合成通路的研究进展

doi:10.16288/j.yczz.23-059

遗传 ›› 2023, Vol. 45 ›› Issue (10): 887-903.doi: 10.16288/j.yczz.23-059

噬菌体Z基因组生物合成通路的研究进展

陈荟玉(), 赵素文()

上海科技大学iHuman研究所与生命科学与技术学院，上海 201210

收稿日期:2023-05-26 修回日期:2023-08-17 出版日期:2023-10-20 发布日期:2023-08-18
通讯作者: 赵素文 E-mail:chenhy6@shanghaitech.edu.cn;zhaosw@shanghaitech.edu.cn
作者简介:陈荟玉，在读硕士研究生，专业方向：计算化学与生物学。E-mail: chenhy6@shanghaitech.edu.cn
基金资助:
国家自然科学基金项目(32122024);上海市生物大分子与精准医药前沿科学研究基地资助

Progress on Z genome biosynthetic pathway of bacteriophage

Huiyu Chen(), Suwen Zhao()

iHuman Institute and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China

Received:2023-05-26 Revised:2023-08-17 Published:2023-10-20 Online:2023-08-18
Contact: Suwen Zhao E-mail:chenhy6@shanghaitech.edu.cn;zhaosw@shanghaitech.edu.cn
Supported by:
National Natural Science Foundation of China(32122024);Shanghai Frontiers Science Center for Bomacromolecules and Precision Medicine

摘要/Abstract

摘要：

噬菌体基因组中存在丰富的碱基修饰，主要用于逃避宿主内切酶的切割。40多年前，在蓝藻噬菌体S-2L的DNA中，研究者发现2-氨基腺嘌呤(Z)完全取代腺嘌呤(A)，与胸腺嘧啶(T)形成具有三根氢键的互补配对，形成了特殊的Z基因组。近年来，研究者在多个噬菌体中发现并证实了噬菌体Z基因组生物合成通路。该通路是一个多酶系统，其中包含由噬菌体DNA编码的2-氨基脱氧腺苷琥珀酸合成酶(PurZ)、脱氧腺苷三磷酸水解酶(dATPase/DatZ)、脱氧腺苷/脱氧鸟苷三磷酸的焦磷酸水解酶(DUF550/MazZ)和DNA聚合酶(DpoZ)。本文在简述噬菌体中各种修饰核苷发现历史的基础上，详细介绍了Z基因组生物合成通路中多种酶的研究进展，最后对Z基因组及其合成通路中多种酶的应用进行了展望，以期为该领域的研究提供借鉴和参考。

关键词: Z基因组, 噬菌体, DNA修饰, 2-氨基腺嘌呤, 生物合成通路

Abstract:

There are abundant base modifications in bacteriophages’ genomes, mainly for avoiding the digestion of host endonucleases. More than 40 years ago, researchers discovered that 2-amino-adenine (Z) completely replaced adenine (A) and forms a complementary pairing with three hydrogen bonds with thymine (T) in the DNA of cyanophage S-2L, forming a distinct “Z-genome”. In recent years, researchers have discovered and validated the biosynthetic pathway of Z-genome in various bacteriophages, constituting a multi-enzyme system. This system includes the phage-encoded enzymes deoxy-2′-aminoadenylosuccinate synthetase (PurZ), deoxyadenosine triphosphate hydrolase (dATPase/DatZ), deoxyadenosine/deoxyguanosine triphosphate pyrophosphatase (DUF550/MazZ) and DNA polymerase (DpoZ). In this review, we provide a concise overview of the historical discovery on diversely modified nucleosides in bacteriophages, then we comprehensively summarize the research progress on multiple enzymes involved in the Z-genome biosynthetic pathway. Finally, the potential applications of the Z-genome and the enzymes in its biosynthetic pathway are discussed in order to provide reference for research in this field.

Key words: Z-genome, bacteriophage, DNA modification, 2-aminoadenine, biosynthetic pathway

陈荟玉, 赵素文. 噬菌体Z基因组生物合成通路的研究进展[J]. 遗传, 2023, 45(10): 887-903.

Huiyu Chen, Suwen Zhao. Progress on Z genome biosynthetic pathway of bacteriophage[J]. Hereditas(Beijing), 2023, 45(10): 887-903.

图/表 9

图1

图2

表1

已分离测序的Z基因组噬菌体名单"

物种名			基因组编号		基因组大小(kb)			GC含量(%)		宿主的物种分类
Ochrobactrum phage vBOspPOH			MT028492.1		41.23			55.2		变形菌门-α变形菌纲-根瘤菌目-布鲁氏菌科-苍白杆菌属
Burkholderia phage BCSR129			MW460247.1		66.15			58.4		变形菌门-β变形菌纲-伯克氏菌目-伯克氏菌科-伯克氏菌属
Salmonella phage PMBT28			MG641885.1		48.11			58.6		变形菌门-γ变形菌纲-肠杆菌目-肠杆菌科-沙门氏菌属
Providencia phage Kokobel2			MW145138.1		45.88			47.5		变形菌门-γ变形菌纲-肠杆菌目-摩根菌科-普罗威登斯菌属
Vibrio phage 23E28 1			MW824387.1		40.73			49.9		变形菌门-γ变形菌纲-弧菌目-弧菌科-弧菌属
Vibrio phage H1			KM612261.1		39.53			50.5		变形菌门-γ变形菌纲-弧菌目-弧菌科-弧菌属
Vibrio phage H2 SGB-2014			KM612262.1		39.53			50.5		变形菌门-γ变形菌纲-弧菌目-弧菌科-弧菌属
Vibrio phage H3			KM612263.1		39.53			50.5		变形菌门-γ变形菌纲-弧菌目-弧菌科-弧菌属
Vibrio phage J3			KM612265.1		39.78			50.5		变形菌门-γ变形菌纲-弧菌目-弧菌科-弧菌属
Vibrio phage QH			KM612259.1		39.73			50.5		变形菌门-γ变形菌纲-弧菌目-弧菌科-弧菌属
Vibrio phage VP5			AY510084.1		39.78			50.5		变形菌门-γ变形菌纲-弧菌目-弧菌科-弧菌属
Vibrio phage CJY			KM612260.1		39.54			50.6		变形菌门-γ变形菌纲-弧菌目-弧菌科-弧菌属
Vibrio phage J2			KM612264.1		39.53			50.6		变形菌门-γ变形菌纲-弧菌目-弧菌科-弧菌属
Vibrio phage JSF33			KY883647.1		39.66			50.6		变形菌门-γ变形菌纲-弧菌目-弧菌科-弧菌属
Vibrio phage JSF9			KY883656.1		40.01			50.6		变形菌门-γ变形菌纲-弧菌目-弧菌科-弧菌属
Vibrio phage VP2			AY5505112		39.85			50.6		变形菌门-γ变形菌纲-弧菌目-弧菌科-弧菌属
Vibrio phage JSF15			KY883642.1		39.64			50.7		变形菌门-γ变形菌纲-弧菌目-弧菌科-弧菌属
Vibrio phage Rostov 6			MH105773.1		39.93			50.7		变形菌门-γ变形菌纲-弧菌目-弧菌科-弧菌属
Vibrio phage phiVC8			JF712866.1		39.42			50.8		变形菌门-γ变形菌纲-弧菌目-弧菌科-弧菌属
Pseudomonas phage PSA28			MZ089737.1		48.44			58.3		变形菌门-γ变形菌纲-假单胞菌目-假单胞菌科-假单胞菌属
Acinetobacter phage Barton			MW176032.1		43.04			47.7		变形菌门-γ变形菌纲-假单胞菌目-莫拉氏菌科-不动杆菌属
Acinetobacter phage DMU1			MT992243.1		43.48			47.8		变形菌门-γ变形菌纲-假单胞菌目-莫拉氏菌科-不动杆菌属
Acinetobacter phage JeffCo			MW176034.1		43.29			47.8		变形菌门-γ变形菌纲-假单胞菌目-莫拉氏菌科-不动杆菌属
Acinetobacter phage SH-Ab 15497			MG674163.1		43.42			47.9		变形菌门-γ变形菌纲-假单胞菌目-莫拉氏菌科-不动杆菌属
Alteromonas phage ZP6^[31]			MK203850.1		37.74			50.1		变形菌门-γ变形菌纲-交替单胞菌目-交替单胞菌科-交替单胞菌属
Gordonia phage Archimedes			MT771339.1		44.94			62.8		放线菌门-放线菌纲-放线菌目-分枝杆菌科-戈登氏菌属
Gordonia phage Ghobes			KX557278.1		45.29			65.2		放线菌门-放线菌纲-放线菌目-分枝杆菌科-戈登氏菌属
Streptomyces phage Hiyaa			MK279841.1		83.22			66.7		放线菌门-放线菌纲-链霉菌目-链霉菌科-链霉菌属
Streptomyces phage Keanu			MT723933.1		82.1			66.8		放线菌门-放线菌纲-链霉菌目-链霉菌科-链霉菌属
Streptomyces phage Galactica			MT316461.1		81.22			66.9		放线菌门-放线菌纲-链霉菌目-链霉菌科-链霉菌属
Curtobacterium phage Parvaparticeps			MZ357096.1		40.29			65.9		放线菌门-放线菌纲-微球菌目-微杆菌科-短小杆菌属
Microbacterium phage FireCastle			Not Found		43			64.8		放线菌门-放线菌纲-微球菌目-微杆菌科-微杆菌属
Microbacterium phage Rasovi			MT310855.1		42.92			65.2		放线菌门-放线菌纲-微球菌目-微杆菌科-微杆菌属
Microbacterium phage PermaG			MZ150782.1		42.28			65.5		放线菌门-放线菌纲-微球菌目-微杆菌科-微杆菌属
Microbacterium phage Theresita			MK660713.1		40.23			65.9		放线菌门-放线菌纲-微球菌目-微杆菌科-微杆菌属
Microbacterium phage Sucha			MK737942.1		41.83			66.1		放线菌门-放线菌纲-微球菌目-微杆菌科-微杆菌属
Microbacterium phage Goodman			MK016495.1		42.36			66.3		放线菌门-放线菌纲-微球菌目-微杆菌科-微杆菌属
Microbacterium phage Johann			MK016497.1		42.36			66.3		放线菌门-放线菌纲-微球菌目-微杆菌科-微杆菌属
Microbacterium phage Cicada		MT498057.1		42.35			66.5				放线菌门-放线菌纲-微球菌目-微杆菌科-微杆菌属
Microbacterium phage SBlackberry		MZ747515.1		42.05			66.9				放线菌门-放线菌纲-微球菌目-微杆菌科-微杆菌属
Microbacterium phage TurboVicky		ON970583.1		42.3			67				放线菌门-放线菌纲-微球菌目-微杆菌科-微杆菌属
Microbacterium phage Typher		ON260821.1		41.86			67				放线菌门-放线菌纲-微球菌目-微杆菌科-微杆菌属
Microbacterium phage Zanella		MN369765.1		42.11			67				放线菌门-放线菌纲-微球菌目-微杆菌科-微杆菌属
Arthrobacter phage DrRobert		KU160643.1		42.6			60.6				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Bodacious		MK112531.1		43.24			60.7				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage ChewChew		MK279844.1		43.44			60.7				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Christian		MF140404.1		43.08			60.7				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage CristinaYang		MK279847.1		43.37			60.7				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage DreamTeam		MK919484.1		43.09			60.7				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Gisselle		MT498050.1		43.09			60.7				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Huntingdon		MG210949.1		43.89			60.7				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Joann		KU160652.1		44.18			60.7				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Kittykat		MW314848.1		43.6			60.7				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Lennox		MK279862.1		43.09			60.7				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage LilStuart		MN813680.1		42.95			60.7				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Lucy		KX576641.1		42.94			60.7				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Nancia		MK279867.1		43.24			60.7				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Nubia		MF140424.1		44.05			60.7				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage OurGirlNessie		MK279869.1		42.56			60.7				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage PitaDog		MF140425.1		42.96			60.7				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Preamble		KU160659.1		43.37			60.7				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage RcigaStruga		KX576640.1		43.89			60.7				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Albanese		OP434444.1		44.11			60.8				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Glenn		KU160645.1		44.39			60.8				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage GreenHearts		MK279854.1		44.25			60.8				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Greenhouse		KX688103.1		43.98			60.8				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Lasagna		MK279860.1		42.6			60.8				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Oxynfrius		KX688102.1		44.16			60.8				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Pterodactyl		MK279872.1		43.27			60.8				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage WonderBoy		Not Found		42.74			60.8				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Fluke		MG198781.1		43.81			60.9				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage MeganNoll		MG198782.1		44.26			60.9				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage MrGloopy		MK660714.1		43.7			60.9				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage RAP15		KU160662.1		44.26			60.9				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Wawa		MK279892.1		43.85			60.9				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Beethoven		MK112528.1		43.93			61				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Carpal		MK112538.1		43.71			61				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Cholula		MK279845.1		43.66			61				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Immaculata		KU160649.1		43.66			61				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Jumboset		OP820465.1		43.78			61				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Potatoes		MK279901.1		43.66			61				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Riverdale		MK279875.1		43.39			61				放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Rozby	MK279876.1					43.2			61			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Savage2526	MK279880.1					43.42			61			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage TattModd	MK279886.1					43.55			61			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Vallejo	KX621005.1					43.61			61			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage AppleCider	MN735429.1					43.7			61.1			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Dino	MF140407.1					43.56			61.1			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Korra	KU160653.2					43.71			61.1			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Litotes	MK279863.1					43.5			61.1			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Scuttle	MK814749.1					43.73			61.1			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Wayne	KU160672.2					44.37			61.1			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Zorro	MK279896.1					43.56			61.1			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage CallieOMalley	MK112535.1					43.86			61.2			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Canowicakte	MF140400.1					43.91			61.2			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Suppi	KX621004.1					43.91			61.2			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Urla	MG198779.1					43.94			61.2			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage BigMack	MK112529.1					43.36			61.3			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage EstebanJulior	MK919476.1					43.75			61.3			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage MamaPearl	MT498045.1					43.75			61.3			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Moki	MH744421.1					43.16			61.3			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Bennie	KU160640.2					43.08			61.4			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage HeadNerd	MK279907.1					42.97			61.4			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Huckleberry	MK279856.1					42.97			61.4			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Stenotrophomonas phage BUCT555	MW291508.1					39.44			61.4			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Chridison	OP751151.1					43.02			61.5			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Eunoia	MK279851.1					44.42			61.5			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Aledel	MK112526.1					43.74			61.6			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage HunterDalle	KU160648.1					43.34			61.6			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage OMalley	MK279868.1					43.74			61.6			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Riovina	MK279874.1					43.74			61.6			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Vulture	KU160671.1					43.34			61.6			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Pumancara	KU160661.1					42.83			61.7			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Supakev	MK279884.1					43.76			61.7			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Daiboju	MH450117.1					43.95			61.9			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Herb	MH450118.1					43.95			61.9			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage KingBob	MH450121.1					43.95			61.9			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Maria1952	MN586061.1					43.95			61.9			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Sergei	MH450131.1					43.95			61.9			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Arthrobacter phage Temper16	MF668285.1					43.95			61.9			放线菌门-放线菌纲-微球菌目-微球菌科-节杆菌属
Phage 66_12	MN304821.1					40.56			66.1			宏基因组
Bacillus phage vB_BpsS-140	MH884512.1					55.09			39.8			厚壁菌门-芽孢杆菌纲-芽孢杆菌目-芽孢杆菌科-芽孢杆菌属
Cyanophage S-2L	AX955019.1					45.57			69.4			蓝藻门

表1

图3

图4

图5

图6

图7

图8

参考文献 50

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噬菌体Z基因组生物合成通路的研究进展

Progress on Z genome biosynthetic pathway of bacteriophage

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